The invention provides a management system and method for water resource regulation and operation, and the management system comprises: a data collection module, which is used for detecting the water affair information and equipment information of the system; a data service module, which is used for counting, analyzing and storing water affair data and equipment data in the system and outputting a management report; a water balance detection module, which is used for monitoring and calculating the water unbalance rate of the system in real time; a salt balance detection module, which is used for monitoring the salt balance condition in real time; and a regulation and control module, which is used for data transmission, analysis, monitoring, early warning, diagnosis and regulation and control of water resources. Through on-line monitoring and regulation of water balance and salt balance, water resources and pollution discharge cost are saved, the situation that water resources are insufficient in the place where a plant is located is relieved, meanwhile, due to the arrangement of the regulation and control module, fault discovery time is greatly shortened, an operator can obtain fault treatment measures in the first time, fault removal time is greatly shortened, and comprehensive water consumption of power generation of the whole plant is reduced.